Contacts of the strand formed by residues 683 - 688 (chain H) in PDB entry 6X34
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 683 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681H HIS* 3.1 49.5 + - - +
682H LEU* 1.3 80.1 - - - +
684H VAL* 1.3 61.0 + - - +
704H GLY 5.5 4.8 + - - -
705H ASN 5.6 0.2 - - - -
706H GLY* 4.9 10.9 - - - +
707H VAL* 3.4 38.1 + - + +
709H ASP* 5.6 3.4 - - - +
715H GLY 5.8 0.9 - - - -
716H PHE 5.3 3.6 - - - +
717H ASP* 3.7 18.2 - - + +
722H TRP* 3.3 68.0 - - - +
725H HIS* 5.6 3.6 + - - -
781H VAL* 3.7 2.7 - - - +
782H SER 3.0 28.6 + - - +
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Residues in contact with VAL 684 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664H PHE* 4.6 24.0 - - + -
666H VAL* 4.7 22.7 - - + -
683H ARG* 1.3 75.1 - - - +
685H GLY* 1.3 63.9 + - - +
707H VAL* 4.7 1.6 - - - -
715H GLY* 4.3 2.0 - - - -
716H PHE 3.2 32.3 + - - +
717H ASP* 5.3 2.7 - - + -
744H VAL* 5.2 12.3 - - + +
745H SER 6.3 1.1 - - - -
746H CYS* 5.7 10.7 - - + +
780H VAL 3.3 14.6 - - - +
781H VAL* 4.2 17.5 - - + +
791H PHE* 5.5 1.3 - - + -
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Residues in contact with GLY 685 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664H PHE* 5.4 0.4 - - - -
684H VAL* 1.3 78.3 - - - +
686H TRP* 1.3 66.1 + - - -
707H VAL* 4.7 8.1 - - - +
714H TYR 3.4 10.8 - - - -
715H GLY* 3.7 6.1 - - - -
746H CYS* 5.5 4.9 - - - -
779H PRO* 3.5 4.5 - - - +
780H VAL* 2.7 41.5 + - - +
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Residues in contact with TRP 686 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650H VAL* 5.4 9.4 - - + -
662H TRP* 4.7 23.6 - + + -
664H PHE* 3.6 29.4 - + - -
685H GLY* 1.3 78.3 - - - -
687H ALA* 1.3 60.1 + - - +
707H VAL* 5.9 1.0 - - - +
713H SER* 3.5 2.9 - - - -
714H TYR* 2.7 42.1 + - + +
746H CYS* 3.0 27.2 - - + +
747H CYS 5.0 0.4 - - - -
748H LEU* 3.5 34.7 - - + +
755H ILE* 4.9 11.4 - - + +
777H PHE* 3.2 47.5 - - + -
778H PHE 3.4 4.3 - - - +
779H PRO* 3.5 31.0 - - + -
811H CYS* 6.0 3.1 - - + -
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Residues in contact with ALA 687 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685H GLY 4.3 0.4 + - - -
686H TRP* 1.3 75.2 - - - +
688H LEU* 1.3 60.9 + - - +
692H TYR* 4.1 23.6 - - + -
707H VAL* 5.3 1.1 - - + -
712H TYR 4.4 0.2 - - - -
713H SER* 3.9 18.6 - - - +
777H PHE* 4.4 3.8 - - - -
778H PHE* 2.9 54.9 + - + +
780H VAL* 4.2 11.4 - - + +
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Residues in contact with LEU 688 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687H ALA* 1.3 75.0 - - - +
689H THR* 1.3 62.7 + - + +
690H GLU 3.3 16.7 + - - +
692H TYR* 4.0 16.9 + - - +
712H TYR* 3.5 24.2 + - + +
775H GLY* 5.8 2.2 - - - -
776H LEU 3.4 16.8 - - - +
777H PHE* 4.3 14.1 - - + -
778H PHE* 3.2 14.3 - - - -
826H ILE* 5.9 0.5 - - - +
1470H ARG* 5.1 7.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il